Question: Complete list of rs ids and thier corresponding sequence for the human genome
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gravatar for Uday Rangaswamy
3 months ago by
Indian Institute of Technology, Madras, India
Uday Rangaswamy100 wrote:

Where can I find a complete list of rs ids and thier corresponding sequence for the human genome?

snp ncbi genome • 177 views
ADD COMMENTlink modified 3 months ago by finswimmer9.8k • written 3 months ago by Uday Rangaswamy100
1
gravatar for finswimmer
3 months ago by
finswimmer9.8k
Germany
finswimmer9.8k wrote:

rs ids are the identification numbers given by dbSNP. So go there and download the vcf file which describes how the bases changes on which position. If you need the padded sequence you could take the fasta files. You could also take the bed files and extract the sequence from the reference genome yourself using e.g. bedtools getfasta.

In the end it depends what you want to do with this data.

fin swimmer

ADD COMMENTlink modified 3 months ago • written 3 months ago by finswimmer9.8k

Agreed. Still, this file will be large (several GB). Therefore, also download the associated tabix index (.vcf.tbi) and spend some quality time reading about the use of tabix to quickly retrieve given genomic regions from large files.

ADD REPLYlink written 3 months ago by ATpoint13k
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